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			<h3 id="dsID"}>dsID</h3><p class='subtitle'>JSON encoded host and dataset id</p><span class="nowrap">/{&quot;host&quot;:&quot;.*&quot;,&quot;name&quot;:&quot;.*&quot;}/</span><br><h3 id="Column"}>Column</h3><p class='subtitle'>A column for display</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>dsID :</td><td class=obj-vals><a href="#dsID"><em>dsID</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>width :</td><td class=obj-vals><span class="it">number [0, &infin;]</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>dataType :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="nowrap">"mutationVector"</span></span> | <span class="inline-block"><span class="nowrap">"geneMatrix"</span></span> | <span class="inline-block"><span class="nowrap">"probeMatrix"</span></span> | <span class="inline-block"><span class="nowrap">"geneProbeMatrix"</span></span> | <span class="inline-block"><span class="nowrap">"clinicalMatrix"</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>fields :</td><td class=obj-vals><span class="align-top">[</span><span class="it">string</span>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>fieldLabel :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>user :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>default :</td><td class=obj-vals><span class="it">string</span>}</td></tr></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>columnLabel :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>user :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>default :</td><td class=obj-vals><span class="it">string</span>}</td></tr></tbody></table>}</td></tr></tbody></table><br><h3 id="Gene"}>Gene</h3><p class='subtitle'>A gene name</p><span class="it">string</span><br><h3 id="Probe"}>Probe</h3><p class='subtitle'>A probe name</p><span class="it">string</span><br><h3 id="Field"}>Field</h3><p class='subtitle'>A gene or probe name</p><p class="inline-block"><span class="inline-block"><a href="#Gene"><em>Gene</em></a></span> | <span class="inline-block"><a href="#Probe"><em>Probe</em></a></span></p><br><h3 id="Chrom"}>Chrom</h3><p class='subtitle'>chrom</p><span class="nowrap">/chr[0-9]+/</span><br><h3 id="Dataset"}>Dataset</h3><p class='subtitle'>Dataset metadata</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>articletitle :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>author :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>citation :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>cohort :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>dataSubType :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="nowrap">"copy number (gene-level)"</span></span> | <span class="inline-block"><span class="nowrap">"somatic non-silent mutation (gene-level)"</span></span> | <span class="inline-block"><span class="nowrap">"gene expression"</span></span> | <span class="inline-block"><span class="nowrap">"phenotype"</span></span> | <span class="inline-block"><span class="nowrap">"somatic mutation (SNPs and small INDELs)"</span></span> | <span class="inline-block"><span class="nowrap">"miRNA expression RNAseq"</span></span> | <span class="inline-block"><span class="nowrap">"DNA methylation"</span></span> | <span class="inline-block"><span class="nowrap">"somatic mutation"</span></span> | <span class="inline-block"><span class="nowrap">"miRNA expression"</span></span> | <span class="inline-block"><span class="nowrap">"exon expression RNAseq"</span></span> | <span class="inline-block"><span class="nowrap">"copy number"</span></span> | <span class="inline-block"><span class="nowrap">"gene expression RNAseq"</span></span> | <span class="inline-block"><span class="nowrap">"PARADIGM pathway activity"</span></span> | <span class="inline-block"><span class="nowrap">"protein expression RPPA"</span></span> | <span class="inline-block"><span class="nowrap">"gene expression array"</span></span> | <span class="inline-block"><span class="nowrap">"somatic mutation (SNP and small INDELs)"</span></span> | <span class="inline-block"><span class="nowrap">"gene expression Array"</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>dataproducer :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>datasubtype :</td><td class=obj-vals><span class="nowrap">"not sure why this is here"</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>description :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>dsID :</td><td class=obj-vals><a href="#dsID"><em>dsID</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>label :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>name :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>server :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>probemap :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="it">string</span></span> | <span class="inline-block"><span class="it">null</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>status :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="nowrap">"loading"</span></span> | <span class="inline-block"><span class="nowrap">"loaded"</span></span> | <span class="inline-block"><span class="nowrap">"error"</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>type :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="nowrap">"genomicMatrix"</span></span> | <span class="inline-block"><span class="nowrap">"genomicSegment"</span></span> | <span class="inline-block"><span class="nowrap">"probeMap"</span></span> | <span class="inline-block"><span class="nowrap">"clinicalMatrix"</span></span> | <span class="inline-block"><span class="nowrap">"genePredExt"</span></span> | <span class="inline-block"><span class="nowrap">"mutationVector"</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>url :</td><td class=obj-vals><span class="it">string</span>}</td></tr></tbody></table><br><h3 id="Feature"}>Feature</h3><p class='subtitle'>Phenotype metdata</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys><a class="it" href="#FeatureName">FeatureName</a> :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>field_id :</td><td class=obj-vals><span class="it">number</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>id :</td><td class=obj-vals><span class="it">number</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>longtitle :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>name :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>priority :</td><td class=obj-vals><span class="it">number [0, &infin;]</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>shorttitle :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>valuetype :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="nowrap">"category"</span></span> | <span class="inline-block"><span class="nowrap">"float"</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>visibility :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="nowrap">"off"</span></span> | <span class="inline-block"><span class="nowrap">"on"</span></span> | <span class="inline-block"><span class="it">null</span></span></p>}</td></tr></tbody></table>, ...}</td></tr></tbody></table><br><h3 id="FeatureID"}>FeatureID</h3><p class='subtitle'>Primary key for a feature</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>dsID :</td><td class=obj-vals><a href="#dsID"><em>dsID</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>name :</td><td class=obj-vals><a href="#FeatureName"><em>FeatureName</em></a>}</td></tr></tbody></table><br><h3 id="FeatureName"}>FeatureName</h3><p class='subtitle'>Name of a feature. Should be unique in the dataset.</p><span class="it">string</span><br><h3 id="FeaturesByDataset"}>FeaturesByDataset</h3><p class='subtitle'>Phenotype metadata, indexed by dataset</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys><a class="it" href="#dsID">dsID</a> :</td><td class=obj-vals><a href="#Feature"><em>Feature</em></a>, ...}</td></tr></tbody></table><br><h3 id="SampleID"}>SampleID</h3><p class='subtitle'>A sample id. Must be unique within a cohort</p><span class="it">string</span><br><h3 id="ColumnID"}>ColumnID</h3><p class='subtitle'>UUID for identifying columns</p><span class="nowrap">/[0-9a-z]{8}-[0-9a-z]{4}-[0-9a-z]{4}-[0-9a-z]{12}/</span><br><h3 id="ColorSpec"}>ColorSpec</h3><p class='subtitle'>A color scale variant.</p><p class="inline-block"><span class="inline-block"><span class="align-top">[</span><span class="nowrap">"float-pos"</span>, <span><span class="it">number</span> <label class='role'>low</label></span>, <span><span class="it">number</span> <label class='role'>high</label></span>, <span><span class="it">number</span> <label class='role'>min</label></span>, <span><span class="it">number</span> <label class='role'>max</label></span>]</span> | <span class="inline-block"><span class="align-top">[</span><span class="nowrap">"float-neg"</span>, <span><span class="it">number</span> <label class='role'>low</label></span>, <span><span class="it">number</span> <label class='role'>high</label></span>, <span><span class="it">number</span> <label class='role'>min</label></span>, <span><span class="it">number</span> <label class='role'>max</label></span>]</span> | <span class="inline-block"><span class="align-top">[</span><span class="nowrap">"float"</span>, <span><span class="it">number</span> <label class='role'>low</label></span>, <span><span class="it">number</span> <label class='role'>zero</label></span>, <span><span class="it">number</span> <label class='role'>high</label></span>, <span><span class="it">number</span> <label class='role'>min</label></span>, <span><span class="it">number</span> <label class='role'>max</label></span>]</span> | <span class="inline-block"><span class="align-top">[</span><span class="nowrap">"float-thresh-pos"</span>, <span><span class="it">number</span> <label class='role'>zero</label></span>, <span><span class="it">number</span> <label class='role'>high</label></span>, <span><span class="it">number</span> <label class='role'>min</label></span>, <span><span class="it">number</span> <label class='role'>threshold</label></span>, <span><span class="it">number</span> <label class='role'>max</label></span>]</span> | <span class="inline-block"><span class="align-top">[</span><span class="nowrap">"float-thresh-neg"</span>, <span><span class="it">number</span> <label class='role'>low</label></span>, <span><span class="it">number</span> <label class='role'>zero</label></span>, <span><span class="it">number</span> <label class='role'>min</label></span>, <span><span class="it">number</span> <label class='role'>threshold</label></span>, <span><span class="it">number</span> <label class='role'>max</label></span>]</span> | <span class="inline-block"><span class="align-top">[</span><span class="nowrap">"float-thresh"</span>, <span><span class="it">number</span> <label class='role'>low</label></span>, <span><span class="it">number</span> <label class='role'>zero</label></span>, <span><span class="it">number</span> <label class='role'>high</label></span>, <span><span class="it">number</span> <label class='role'>min</label></span>, <span><span class="it">number</span> <label class='role'>minThreshold</label></span>, <span><span class="it">number</span> <label class='role'>maxThreshold</label></span>, <span><span class="it">number</span> <label class='role'>max</label></span>]</span> | <span class="inline-block"><span class="align-top">[</span><span class="nowrap">"ordinal"</span>, <span><span class="it">number [0, &infin;]</span> <label class='role'>count</label></span>]</span></p><br><h3 id="HeatmapData"}>HeatmapData</h3><p class='subtitle'>Matrix of values for heatmap display, ordered by field and sample.</p><span class="align-top">[</span><span><span class="align-top">[</span><span><span class="it">number</span> <label class='role'>sample</label></span>, ...] <label class='role'>field</label></span>, ...]<br><h3 id="ProbeData"}>ProbeData</h3><p class='subtitle'>Data for a probe column</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>req :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>mean :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys><a class="it" href="#Field">Field</a> :</td><td class=obj-vals><span class="it">number</span>, ...}</td></tr></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>probes :</td><td class=obj-vals><span class="align-top">[</span><span class="it">string</span>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>values :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys><a class="it" href="#Field">Field</a> :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys><a class="it" href="#SampleID">SampleID</a> :</td><td class=obj-vals><span class="it">number</span>, ...}</td></tr></tbody></table>, ...}</td></tr></tbody></table>}</td></tr></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>features :</td><td class=obj-vals><a href="#Feature"><em>Feature</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>codes :</td><td class=obj-vals><span class="align-top">[</span><span class="nowrap">"FIXME"</span>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>bounds :</td><td class=obj-vals><span class="align-top">[</span><span class="nowrap">"FIXME"</span>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>display :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>colors :</td><td class=obj-vals><span class="align-top">[</span><a href="#ColorSpec"><em>ColorSpec</em></a>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>heatmap :</td><td class=obj-vals><a href="#HeatmapData"><em>HeatmapData</em></a>}</td></tr></tbody></table>}</td></tr></tbody></table><br><h3 id="BasePosition"}>BasePosition</h3><p class='subtitle'>Base position</p><span class="it">number [0, &infin;]</span><br><h3 id="Sequence"}>Sequence</h3><p class='subtitle'>String representation of a sequence</p><span class="nowrap">/[ACTG]*/</span><br><h3 id="RefGene"}>RefGene</h3><p class='subtitle'>A refGene annotation</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>cdsEnd :</td><td class=obj-vals><a href="#BasePosition"><em>BasePosition</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>cdsStart :</td><td class=obj-vals><a href="#BasePosition"><em>BasePosition</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>exonCount :</td><td class=obj-vals><span class="it">number [0, &infin;]</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>exonEnds :</td><td class=obj-vals><span class="align-top">[</span><a href="#BasePosition"><em>BasePosition</em></a>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>exonStarts :</td><td class=obj-vals><span class="align-top">[</span><a href="#BasePosition"><em>BasePosition</em></a>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>name2 :</td><td class=obj-vals><a href="#Gene"><em>Gene</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>strand :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="it">null</span></span> | <span class="inline-block"><span class="nowrap">"-"</span></span> | <span class="inline-block"><span class="nowrap">"+"</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>txEnd :</td><td class=obj-vals><a href="#BasePosition"><em>BasePosition</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>txStart :</td><td class=obj-vals><a href="#BasePosition"><em>BasePosition</em></a>}</td></tr></tbody></table><br><h3 id="Mutation"}>Mutation</h3><p class='subtitle'>Mutation record</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>alt :</td><td class=obj-vals><a href="#Sequence"><em>Sequence</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>amino_acid :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>chr :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>dna_vaf :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="it">null</span></span> | <span class="inline-block"><span class="it">number</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>effect :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>end :</td><td class=obj-vals><a href="#BasePosition"><em>BasePosition</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>gene :</td><td class=obj-vals><a href="#Gene"><em>Gene</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>reference :</td><td class=obj-vals><a href="#Sequence"><em>Sequence</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>rna_vaf :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="it">null</span></span> | <span class="inline-block"><span class="it">number</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>sample :</td><td class=obj-vals><a href="#SampleID"><em>SampleID</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>start :</td><td class=obj-vals><a href="#BasePosition"><em>BasePosition</em></a>}</td></tr></tbody></table><br><h3 id="MutationData"}>MutationData</h3><p class='subtitle'>Data for a mutation column</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>req :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>samples :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys><a class="it" href="#SampleID">SampleID</a> :</td><td class=obj-vals><span class="it">boolean</span>, ...}</td></tr></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>rows :</td><td class=obj-vals><span class="align-top">[</span><a href="#Mutation"><em>Mutation</em></a>, ...]}</td></tr></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>refGene :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys><a class="it" href="#Field">Field</a> :</td><td class=obj-vals><a href="#RefGene"><em>RefGene</em></a>, ...}</td></tr></tbody></table>}</td></tr></tbody></table><br><h3 id="MutationViewData"}>MutationViewData</h3><p class='subtitle'>Data for the mutation view</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>index :</td><td class=obj-vals><table class='obj'><tbody></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>order :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys><a class="it" href="#SampleID">SampleID</a> :</td><td class=obj-vals>0, ...}</td></tr></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>refGene :</td><td class=obj-vals><a href="#RefGene"><em>RefGene</em></a>}</td></tr></tbody></table><br><h3 id="VizSettings"}>VizSettings</h3><p class='subtitle'>User settings for visualization</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>max :</td><td class=obj-vals><span class="it">number</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>maxStart :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="it">number</span></span> | <span class="inline-block"><span class="it">null</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>minStart :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="it">number</span></span> | <span class="inline-block"><span class="it">null</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>min :</td><td class=obj-vals><span class="it">number</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>colNormalization :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="it">boolean</span></span> | <span class="inline-block"><span class="it">null</span></span></p>}</td></tr></tbody></table><br><h3 id="Application"}>Application</h3><p class='subtitle'>The application state</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>cohort :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>cohorts :</td><td class=obj-vals><span class="align-top">[</span><span class="it">string</span>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>columnOrder :</td><td class=obj-vals><span class="align-top">[</span><a href="#ColumnID"><em>ColumnID</em></a>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>columns :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys><a class="it" href="#ColumnID">ColumnID</a> :</td><td class=obj-vals><a href="#Column"><em>Column</em></a>, ...}</td></tr></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>data :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys><a class="it" href="#ColumnID">ColumnID</a> :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><a href="#ProbeData"><em>ProbeData</em></a></span> | <span class="inline-block"><a href="#MutationData"><em>MutationData</em></a></span></p>, ...}</td></tr></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>datasets :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys><a class="it" href="#dsID">dsID</a> :</td><td class=obj-vals><a href="#Dataset"><em>Dataset</em></a>, ...}</td></tr></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>features :</td><td class=obj-vals><a href="#FeaturesByDataset"><em>FeaturesByDataset</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>km :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>id :</td><td class=obj-vals><a href="#ColumnID"><em>ColumnID</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>column :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><a href="#ProbeData"><em>ProbeData</em></a></span> | <span class="inline-block"><a href="#MutationData"><em>MutationData</em></a></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>label :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>vars :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>event :</td><td class=obj-vals><a href="#FeatureID"><em>FeatureID</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>patient :</td><td class=obj-vals><a href="#FeatureID"><em>FeatureID</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>tte :</td><td class=obj-vals><a href="#FeatureID"><em>FeatureID</em></a>}</td></tr></tbody></table>}</td></tr></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>samples :</td><td class=obj-vals><span class="align-top">[</span><span class="it">string</span>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>samplesFrom :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="it">string</span></span> | <span class="inline-block"><span class="it">null</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>servers :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>default :</td><td class=obj-vals><span class="align-top">[</span><span class="it">string</span>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>user :</td><td class=obj-vals><span class="align-top">[</span><span class="it">string</span>, ...]}</td></tr></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>zoom :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>count :</td><td class=obj-vals><span class="it">number [0, &infin;]</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>height :</td><td class=obj-vals><span class="it">number [0, &infin;]</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>index :</td><td class=obj-vals><span class="it">number [0, &infin;]</span>}</td></tr></tbody></table></td></tr><tr><td class=obj-name></td><td class=obj-keys>vizSettings :</td><td class=obj-vals><a href="#VizSettings"><em>VizSettings</em></a>}</td></tr></tbody></table><br><h3 id="ChromLayout"}>ChromLayout</h3><p class='subtitle'>A chromosome layout. Currently limited to a single chrom.</p><span class="align-top">[</span><span class="align-top">[</span><span><span class="it">number [0, &infin;]</span> <label class='role'>start</label></span>, <span><span class="it">number [0, &infin;]</span> <label class='role'>end</label></span>], ...]<br><h3 id="ScreenLayout"}>ScreenLayout</h3><p class='subtitle'>A screen layout</p><span class="align-top">[</span><span class="align-top">[</span><span><span class="it">number [0, &infin;]</span> <label class='role'>start px</label></span>, <span><span class="it">number [0, &infin;]</span> <label class='role'>end px</label></span>], ...]<br><h3 id="Layout"}>Layout</h3><p class='subtitle'>Screen and chrom layout</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>chrom :</td><td class=obj-vals><a href="#ChromLayout"><em>ChromLayout</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>screen :</td><td class=obj-vals><a href="#ScreenLayout"><em>ScreenLayout</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>reversed :</td><td class=obj-vals><span class="it">boolean</span>}</td></tr></tbody></table><br><h3 id="colorString"}>colorString</h3><p class='subtitle'>A css color string</p><p class="inline-block"><span class="inline-block"><span class="nowrap">/#[0-9A-Fa-f]{6}/</span></span> | <span class="inline-block"><span class="it">string</span></span></p><br><h3 id="KmPoint"}>KmPoint</h3><p class='subtitle'>A time point in a KM result. t: time; s: % surviving at t; e: event at t</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>d :</td><td class=obj-vals><span class="it">number</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>e :</td><td class=obj-vals><span><span class="it">boolean</span> <label class='role'>event at time t</label></span></td></tr><tr><td class=obj-name></td><td class=obj-keys>n :</td><td class=obj-vals><span><span class="it">number</span> <label class='role'>number in study at time t</label></span></td></tr><tr><td class=obj-name></td><td class=obj-keys>rate :</td><td class=obj-vals><p class="inline-block"><span class="inline-block"><span class="it">null</span></span> | <span class="inline-block"><span class="it">number</span></span></p></td></tr><tr><td class=obj-name></td><td class=obj-keys>s :</td><td class=obj-vals><span><span class="it">number</span> <label class='role'>% surviving at time t</label></span></td></tr><tr><td class=obj-name></td><td class=obj-keys>t :</td><td class=obj-vals><span><span class="it">number</span> <label class='role'>time</label></span>}</td></tr></tbody></table><br><h3 id="KmPlotData"}>KmPlotData</h3><p class='subtitle'>Data for drawing KM</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>ev :</td><td class=obj-vals><a href="#FeatureID"><em>FeatureID</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>tte :</td><td class=obj-vals><a href="#FeatureID"><em>FeatureID</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>patient :</td><td class=obj-vals><a href="#FeatureID"><em>FeatureID</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>id :</td><td class=obj-vals><a href="#ColumnID"><em>ColumnID</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>label :</td><td class=obj-vals><span class="it">string</span></td></tr><tr><td class=obj-name></td><td class=obj-keys>groups :</td><td class=obj-vals><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>colors :</td><td class=obj-vals><span class="align-top">[</span><a href="#colorString"><em>colorString</em></a>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>labels :</td><td class=obj-vals><span class="align-top">[</span><span class="it">string</span>, ...]</td></tr><tr><td class=obj-name></td><td class=obj-keys>curves :</td><td class=obj-vals><span class="align-top">[</span><span class="align-top">[</span><a href="#KmPoint"><em>KmPoint</em></a>, ...], ...]}</td></tr></tbody></table>}</td></tr></tbody></table><br><h3 id="KmPlotProps"}>KmPlotProps</h3><p class='subtitle'>KmPlot Component properties</p><table class='obj'><tbody><tr><td class=obj-name>{</td><td class=obj-keys>callback :</td><td class=obj-vals><span><span>fn(<a href="#Action"><em>Action</em></a>)</span> <label class='role'>State updater</label></span></td></tr><tr><td class=obj-name></td><td class=obj-keys>eventClose :</td><td class=obj-vals><span><span class="it">string</span> <label class='role'>Action type to issue on &quot;close&quot;</label></span></td></tr><tr><td class=obj-name></td><td class=obj-keys>features :</td><td class=obj-vals><a href="#FeaturesByDataset"><em>FeaturesByDataset</em></a></td></tr><tr><td class=obj-name></td><td class=obj-keys>km :</td><td class=obj-vals><a href="#KmPlotData"><em>KmPlotData</em></a>}</td></tr></tbody></table><br><h3 id="Action"}>Action</h3><p class='subtitle'>Action on state</p><span class="align-top">[</span><span><span class="it">string</span> <label class='role'>type</label></span>, ...]
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